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    Protocols in Current Issue
    Tethered Chromosome Conformation Capture Sequencing in Triticeae: A Valuable Tool for Genome Assembly
    Authors:  Axel Himmelbach, Ines Walde, Martin Mascher and Nils Stein, date: 08/05/2018, view: 161, Q&A: 0
    Chromosome conformation capture sequencing (Hi-C) is a powerful method to comprehensively interrogate the three-dimensional positioning of chromatin in the nucleus. The development of Hi-C can be traced back to successive increases in the resolution ...
    Hypoxia Reporter Element Assay
    Authors:  Daelynn R Buelow and Sharyn D. D Baker, date: 08/05/2018, view: 105, Q&A: 0
    Hypoxia is a condition in which there is a decrease in oxygen supply to the cellular environment. Changes to cellular oxygen levels can lead to transcriptional changes of oxygen-regulated genes. Reporter assays are used to study gene expression ...
    Measuring Secretion of Capsidiol in Leaf Tissues of Nicotiana benthamiana
    Authors:  Teruhiko Kuroyanagi, Maurizio Camagna and Daigo Takemoto, date: 08/05/2018, view: 129, Q&A: 0
    Plant species produce a wide variety of antimicrobial metabolites to protect themselves against potential pathogens in natural environments. Phytoalexins are low molecular weight compounds produced by plants in response to attempted attacks of ...
    Fusarium graminearum Inoculation on Wheat Head
    Authors:  Chanjing Feng, Huiquan Liu and Zhe Tang, date: 08/05/2018, view: 117, Q&A: 0
    Fusarium graminearum, the major causal agent of Fusarium head blight (FHB), causes serious wheat yield losses and a threat to human and animal health. The main efforts to combat the disease are the research of pathogenesis ...
    Direct Visualization of the Multicopy Chromosomes in Cyanobacterium Synechococcus elongatus PCC 7942
    Authors:  Ryudo Ohbayashi, Hirofumi Yoshikawa and Satoru Watanabe, date: 08/05/2018, view: 120, Q&A: 0
    Cyanobacteria are prokaryotic organisms that carry out oxygenic photosynthesis. The fresh water cyanobacterium Synechococcus elongatus PCC 7942 is a model organism for the study of photosynthesis and gene regulation, and for ...
    Tethered Chromosome Conformation Capture Sequencing in Triticeae: A Valuable Tool for Genome Assembly
    Authors:  Axel Himmelbach, Ines Walde, Martin Mascher and Nils Stein, date: 08/05/2018, view: 161, Q&A: 0
    [Abstract] Chromosome conformation capture sequencing (Hi-C) is a powerful method to comprehensively interrogate the three-dimensional positioning of chromatin in the nucleus. The development of Hi-C can be traced back to successive increases in the resolution and throughput of chromosome conformation capture (3C) (Dekker et al., 2002). The basic ...
    Hypoxia Reporter Element Assay
    Authors:  Daelynn R Buelow and Sharyn D. D Baker, date: 08/05/2018, view: 105, Q&A: 0
    [Abstract] Hypoxia is a condition in which there is a decrease in oxygen supply to the cellular environment. Changes to cellular oxygen levels can lead to transcriptional changes of oxygen-regulated genes. Reporter assays are used to study gene expression alteration and modifications in response to environmental changes. Dual-reporter assays allow the ...
    Measuring Secretion of Capsidiol in Leaf Tissues of Nicotiana benthamiana
    Authors:  Teruhiko Kuroyanagi, Maurizio Camagna and Daigo Takemoto, date: 08/05/2018, view: 129, Q&A: 0
    [Abstract] Plant species produce a wide variety of antimicrobial metabolites to protect themselves against potential pathogens in natural environments. Phytoalexins are low molecular weight compounds produced by plants in response to attempted attacks of pathogens. Accumulation of phytoalexins in attacked plant tissues can inhibit the growth of penetrating ...
    Fusarium graminearum Inoculation on Wheat Head
    Authors:  Chanjing Feng, Huiquan Liu and Zhe Tang, date: 08/05/2018, view: 117, Q&A: 0
    [Abstract] Fusarium graminearum, the major causal agent of Fusarium head blight (FHB), causes serious wheat yield losses and a threat to human and animal health. The main efforts to combat the disease are the research of pathogenesis mechanisms and breeding for disease resistance plants. The efficiency of these actions could be evaluated by ...
    Direct Visualization of the Multicopy Chromosomes in Cyanobacterium Synechococcus elongatus PCC 7942
    Authors:  Ryudo Ohbayashi, Hirofumi Yoshikawa and Satoru Watanabe, date: 08/05/2018, view: 120, Q&A: 0
    [Abstract] Cyanobacteria are prokaryotic organisms that carry out oxygenic photosynthesis. The fresh water cyanobacterium Synechococcus elongatus PCC 7942 is a model organism for the study of photosynthesis and gene regulation, and for biotechnological applications. Besides several freshwater cyanobacteria, S. elongatus 7942 also contains ...
    In vitro Enzymatic Assays of Histone Decrotonylation on Recombinant Histones
    Authors:  Rachel Fellows and Patrick Varga-Weisz, date: 07/20/2018, view: 321, Q&A: 0
    [Abstract] Class I histone deacetylases (HDACs) are efficient histone decrotonylases, broadening the enzymatic spectrum of these important (epi-)genome regulators and drug targets. Here, we describe an in vitro approach to assaying class I HDACs with different acyl-histone substrates, including crotonylated histones and expand this to examine the ...
    α-Synuclein Aggregation Monitored by Thioflavin T Fluorescence Assay
    Authors:  Michael M. Wördehoff and Wolfgang Hoyer, date: 07/20/2018, view: 377, Q&A: 0
    [Abstract] Studying the aggregation of amyloid proteins like α-synuclein in vitro is a convenient and popular tool to gain kinetic insights into aggregation as well as to study factors (e.g., aggregation inhibitors) that influence it. These aggregation assays typically make use of the fluorescence dye Thioflavin T as a sensitive ...
    High Resolution Melting Temperature Analysis to Identify CRISPR/Cas9 Mutants from Arabidopsis
    Authors:  Cynthia Denbow, Sonia Carole Ehivet and Sakiko Okumoto, date: 07/20/2018, view: 247, Q&A: 0
    [Abstract] CRISPR/Cas9 made targeted mutagenesis and genome editing possible for many plant species. One of the ways that the endonuclease is used for plant genetics is the creation of loss-of-function mutants, which typically result from erroneous DNA repair through non-homologous end joining (NHEJ) pathway. The majority of erroneous repair events results ...
    Extraction of RNA from Recalcitrant Tree Species Paulownia elongata
    Authors:  Niveditha Ramadoss and Chhandak Basu, date: 07/20/2018, view: 259, Q&A: 0
    [Abstract] Isolation of pure RNA is the basic requisite for most molecular biology work. Plants contain polyphenols and polysaccharides, which can interfere with isolation of pure RNA from them. Especially hardwood tree species like Paulownia elongata have surplus amount of RNA-binding alkaloids, proteins and secondary metabolites that can further ...
    Single and Multiplexed Gene Editing in Ustilago maydis Using CRISPR-Cas9
    [Abstract] The smut fungus Ustilago maydis is an established model organism for elucidating how biotrophic pathogens colonize plants and how gene families contribute to virulence. Here we describe a step by step protocol for the generation of CRISPR plasmids for single and multiplexed gene editing in U. maydis. Furthermore, we describe the ...